GEO DataSets

(Submitter supplied) The purpose of this experiment was to determine the genes directly regulated by Ste12 in K. lactis. The experiment was performed in a cells to determine if the a-specific genes were bound by Ste12. Ste12 was tagged with c-myc and was immunoprecipitated with a c-myc antibody. Cells were starved in SD media lacking phosphate for 2 hours, then treated with 10µg/mL K. lactis alpha factor for 2 hours before harvesting. more...

Organism:

Kluyveromyces lactis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19759

4 Samples

Download data: BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9134 GPL9825

222 Samples

Download data: TXT

(Submitter supplied) In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9134

174 Samples

Download data: TXT

(Submitter supplied) In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c, as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9825

48 Samples

Download data: TXT

(Submitter supplied) PCR products from promoter regions

Organism:

Homo sapiens

1 Series

8 Samples

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(Submitter supplied) A fundamental problem in biology is the molecular basis for divergence among related organisms. We have investigated the level of divergence of transcription factor binding sites for two key factors that regulate developmental processes in the budding yeasts. The genomic binding locations for the Ste12 and Tec1 transcription factors in S. cerevisiae, S. mikatae and S. bayanus were mapped by chromatin immunoprecipitation combined with microarrays (chIP chip)1, 2 and compared to one another. more...

Organism:

Saccharomyces cerevisiae; Candida albicans; Saccharomyces mikatae; Saccharomyces bayanus

Type:

Genome binding/occupancy profiling by genome tiling array

4 related Platforms

27 Samples

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(Submitter supplied) ChIP-chip to determine the regulation of the K. lactis hsgs (ChIP of MATa1, MATalpha2, and RME1). The MATa1 and MATalpha2 ChIPs were performed in an a/alpha cell using N-terminally HA-tagged proteins and the RME1 ChIPs were perfomed in an a cell using C-terminally myc-tagged protein. For the RME1 ChIPs, the cells grown with out phosphate. For the MATa1 andMATalpha2 ChIPs the cells were grown in YEPD.

Organism:

Kluyveromyces lactis NRRL Y-1140; Kluyveromyces lactis

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL11182

6 Samples

Download data: GPR

(Submitter supplied) WT and rme1 KO K. lactis cells (a, alpha, and a/alpha) were grown in YEPD, phosphate starvation and phosphate starvation with the addition of alpha pheromone. The goal was to identify cell-type regulated genes and to determine the effects of growth media on the regulation of cell-type regulated genes

Organism:

Kluyveromyces lactis

Type:

Expression profiling by array

Platform:

GPL10962

20 Samples

Download data: GPR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Nakaseomyces glabratus; Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL22622 GPL13821

62 Samples

Download data: WIG

(Submitter supplied) In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. more...

Organism:

Nakaseomyces glabratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22622

8 Samples

Download data: CSV

(Submitter supplied) In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

36 Samples

Download data: CSV

(Submitter supplied) In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. more...

Organism:

Nakaseomyces glabratus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22622

9 Samples

Download data: WIG

(Submitter supplied) In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

9 Samples

Download data: WIG

(Submitter supplied) Although global analyses of transcription factor binding provide one view of potential transcriptional regulatory networks, regulation also occurs at levels distinct from transcription factor binding. Here, we use a genetic approach to identify targets of transcription factors in yeast and reconstruct a functional regulatory network. First, we profiled transcriptional responses in S. cerevisiae strains with individual deletions of 263 transcription factors. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL3588

269 Samples

Download data

(Submitter supplied) Here we show that the ChEC-Seq technique is able to differentiate the binding specificities of Esa1 and Gcn5 two chromatin-binding factors displaying widespread genome-wide associations. We also show that the ChEC-Seq technique reveals strong binding of the transcription factor Sfp1 at Ribi gene promoters. Furthermore, our data provide the first evidence that a specific DNA motif previously identified by ChEC-Seq (Albert 2019 PMID: 30804227) is in fact an in vivo binding site for Sfp1.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

10 Samples

Download data: BW

(Submitter supplied) Understanding how transcriptional programs help to coordinate cell growth and division is an important unresolved problem. Here we report that the nutrient- and stress-regulated transcription factor Sfp1 is rate-limiting for expression of a large suite of genes involved in yeast cell growth, including ribosomal protein, ribosome biogenesis, and snoRNA genes. Remarkably, the spectrum of Sfp1 transcription effects is concordant with a combination of chromatin immunoprecipitation and chromatin endogenous cleavage binding analyses, which together provide evidence for two distinct modes of Sfp1 promoter binding, one requiring a co-factor and the other a specific DNA-recognition motif. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

32 Samples

Download data: BIGWIG, BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli; Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL18133 GPL17342

38 Samples

Download data: TXT

(Submitter supplied) Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure the cis-regulatory consequences of 5,832 natural DNA variants in the promoters of 2,503 genes in the yeast Saccharomyces cerevisiae. We identified 451 causal variants, which underlie genetic loci known to affect gene expression. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

36 Samples

Download data: TXT

(Submitter supplied) Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure the cis-regulatory consequences of 5,832 natural DNA variants in the promoters of 2,503 genes in the yeast Saccharomyces cerevisiae. We identified 451 causal variants, which underlie genetic loci known to affect gene expression. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL18133

2 Samples

Download data: TXT

(Submitter supplied) Here, we examine how six single amino acid variants in the DNA-binding domain of Ste12 – a yeast transcription factor regulating mating and invasion – alter Ste12 genome binding, motif recognition and gene expression to yield markedly different phenotypes. Using a combination of the calling card method, RNA sequencing , we find that variants with dissimilar binding and expression profiles can converge onto similar cellular behaviors.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19756

18 Samples

Download data: TXT